This review analyzes published data on manure management practices used to mitigate methane (CH4) and nitrous oxide (N2O) emissions from animal operations. Reducing excreted nitrogen (N) and degradable organic carbon (C) by diet manipulation to improve the balance of nutrient inputs with production is an effective practice to reduce CH4 and N2O emissions. Most CH4 is produced during manure storage; therefore, reducing storage time, lowering manure temperature by storing it outside during colder seasons, and capturing and combusting the CH4 produced during storage are effective practices to reduce CH4 emission. Anaerobic digestion with combustion of the gas produced is effective in reducing CH4 emission and organic C content of manure; this increases readily available C and N for microbial processes creating little CH4 and increased N2O emissions following land application. Nitrous oxide emission occurs following land application as a byproduct of nitrification and dentrification processes in the soil, but these processes may also occur in compost, biofilter materials, and permeable storage covers. These microbial processes depend on temperature, moisture content, availability of easily degradable organic C, and oxidation status of the environment, which make N2O emissions and mitigation results highly variable. Managing the fate of ammoniacal N is essential to the success of N2O and CH4 mitigation because ammonia is an important component in the cycling of N through manure, soil, crops, and animal feeds. Manure application techniques such as subsurface injection reduce ammonia and CH4 emissions but can result in increased N2O emissions. Injection works well when combined with anaerobic digestion and solids separation by improving infiltration. Additives such as urease and nitrification inhibitors that inhibit microbial processes have mixed results but are generally effective in controlling N2O emission from intensive grazing systems. Matching plant nutrient requirements with manure fertilization, managing grazing intensity, and using cover crops are effective practices to increase plant N uptake and reduce N2O emissions. Due to system interactions, mitigation practices that reduce emissions in one stage of the manure management process may increase emissions elsewhere, so mitigation practices must be evaluated at the whole farm level.